Some libraries aren't paired end so their library ids will be missing from
the list, leaving holes in the array.

Still, I've arranged this recently so that the paired end libraries always
come first. Plus, I could leave the missing entries as null values.
On Dec 15, 2013 8:19 PM, "Jianfeng Jia" <notifications@github.com> wrote:

> In
> genomix/genomix-data/src/main/java/edu/uci/ics/genomix/data/config/GenomixJobConf.java:
>
> >          Byte libraryId = 0;
> >          if (conf.get(OUTER_DISTANCE_MEANS) != null) {
> > +            outerDistanceMeans = new HashMap<>();
> >              for (String mean : conf.get(OUTER_DISTANCE_MEANS).split(",")) {
> >                  outerDistanceMeans.put(libraryId++, Integer.valueOf(mean));
>
> If the libraryId is just ++, why we use the HashMap?
>
> —
> Reply to this email directly or view it on GitHub<https://github.com/uci-cbcl/genomix/pull/101/files#r8358724>
> .
>